Pairwise Comparisons (GSE137001)

Pathway Heatmap

# Get enrichr results and save to file
padj_cutoff <- 0.01
lfc_cutoff <- 0.5
dbs <- c("GO_Biological_Process_2021")

if (!file.exists("enriched_res.Rdata")) {
  enriched_res <- lapply(lfc_dfs, function(df) {
    genes <- df %>%
      filter(padj <= padj_cutoff & abs(log2FoldChange) >= lfc_cutoff) %>%
      pull(SYMBOL)
    
    return(enrichr(genes, dbs))
  })
  save(enriched_res, file = "enriched_res.Rdata")
} else {
  load("enriched_res.Rdata")
}

# Extract combined scores from each enrichr result
combined_scores <- lapply(enriched_res, function(res) {
  c_score <- res[["GO_Biological_Process_2021"]] %>%
    filter(str_detect(Term, paste(pathways, collapse="|"))) %>%
    arrange(Term) %>% 
    pull(Combined.Score)
  
  return(c_score)
})

combined_scores <- as.data.frame(combined_scores)

row.names(combined_scores) <- enriched_res[[1]][["GO_Biological_Process_2021"]] %>%
  filter(str_detect(Term, paste(pathways, collapse="|"))) %>%
  arrange(Term) %>%
  pull(Term)

enriched_res[[1]][["GO_Biological_Process_2021"]] %>%
  filter(str_detect(Term, paste(pathways, collapse="|"))) %>%
  arrange(Term) %>%
  pull(Term)

[1] "ATF6-mediated unfolded protein response (GO:0036500)"                                                   
[2] "cellular response to amino acid starvation (GO:0034198)"                                                
[3] "cellular response to oxidative stress (GO:0034599)"                                                     
[4] "cellular response to starvation (GO:0009267)"                                                           
[5] "macroautophagy (GO:0016236)"                                                                            
[6] "positive regulation of transcription from RNA polymerase II promoter in response to stress (GO:0036003)"
[7] "regulation of autophagy (GO:0010506)"                                                                   
[8] "response to amino acid starvation (GO:1990928)"                                                         
[9] "response to endoplasmic reticulum stress (GO:0034976)"                                                  

DEG Datatables and Volcano Plots

d2_vs_MEF

# Datatable example
res <- lfc_dfs[[1]]
padj_cutoff <- 0.01
lfc_cutoff <- 0.5

res %>%
  select(SYMBOL, log2FoldChange, padj) %>%
  filter(padj <= padj_cutoff & abs(log2FoldChange) >= lfc_cutoff) %>%
  arrange(padj) %>% 
  DT::datatable() %>%
  DT::formatSignif(columns = 2:3, digits = 3)

# Volcano plot example
EnhancedVolcano::EnhancedVolcano(
  res,
  lab = res$SYMBOL,
  x = "log2FoldChange",
  y = "padj",
  pCutoff = padj_cutoff,
  FCcutoff = lfc_cutoff,
  subtitle = sprintf(
    "Adjusted p-value cutoff = %0.2f
|Log2FoldChange| cutoff = %0.1f",
    padj_cutoff, lfc_cutoff
  )
)

d4_vs_MEF

# Datatable example
res <- lfc_dfs[[2]]
padj_cutoff <- 0.01
lfc_cutoff <- 0.5

res %>%
  select(SYMBOL, log2FoldChange, padj) %>%
  filter(padj <= padj_cutoff & abs(log2FoldChange) >= lfc_cutoff) %>%
  arrange(padj) %>% 
  DT::datatable() %>%
  DT::formatSignif(columns = 2:3, digits = 3)

# Volcano plot example
EnhancedVolcano::EnhancedVolcano(
  res,
  lab = res$SYMBOL,
  x = "log2FoldChange",
  y = "padj",
  pCutoff = padj_cutoff,
  FCcutoff = lfc_cutoff,
  subtitle = sprintf(
    "Adjusted p-value cutoff = %0.2f
|Log2FoldChange| cutoff = %0.1f",
    padj_cutoff, lfc_cutoff
  )
)

d6_vs_MEF

# Datatable example
res <- lfc_dfs[[3]]
padj_cutoff <- 0.01
lfc_cutoff <- 0.5

res %>%
  select(SYMBOL, log2FoldChange, padj) %>%
  filter(padj <= padj_cutoff & abs(log2FoldChange) >= lfc_cutoff) %>%
  arrange(padj) %>% 
  DT::datatable() %>%
  DT::formatSignif(columns = 2:3, digits = 3)

# Volcano plot example
EnhancedVolcano::EnhancedVolcano(
  res,
  lab = res$SYMBOL,
  x = "log2FoldChange",
  y = "padj",
  pCutoff = padj_cutoff,
  FCcutoff = lfc_cutoff,
  subtitle = sprintf(
    "Adjusted p-value cutoff = %0.2f
|Log2FoldChange| cutoff = %0.1f",
    padj_cutoff, lfc_cutoff
  )
)

d9_vs_MEF

# Datatable example
res <- lfc_dfs[[4]]
padj_cutoff <- 0.01
lfc_cutoff <- 0.5

res %>%
  select(SYMBOL, log2FoldChange, padj) %>%
  filter(padj <= padj_cutoff & abs(log2FoldChange) >= lfc_cutoff) %>%
  arrange(padj) %>% 
  DT::datatable() %>%
  DT::formatSignif(columns = 2:3, digits = 3)

# Volcano plot example
EnhancedVolcano::EnhancedVolcano(
  res,
  lab = res$SYMBOL,
  x = "log2FoldChange",
  y = "padj",
  pCutoff = padj_cutoff,
  FCcutoff = lfc_cutoff,
  subtitle = sprintf(
    "Adjusted p-value cutoff = %0.2f
|Log2FoldChange| cutoff = %0.1f",
    padj_cutoff, lfc_cutoff
  )
)

d12_vs_MEF

# Datatable example
res <- lfc_dfs[[5]]
padj_cutoff <- 0.01
lfc_cutoff <- 0.5

res %>%
  select(SYMBOL, log2FoldChange, padj) %>%
  filter(padj <= padj_cutoff & abs(log2FoldChange) >= lfc_cutoff) %>%
  arrange(padj) %>% 
  DT::datatable() %>%
  DT::formatSignif(columns = 2:3, digits = 3)

# Volcano plot example
EnhancedVolcano::EnhancedVolcano(
  res,
  lab = res$SYMBOL,
  x = "log2FoldChange",
  y = "padj",
  pCutoff = padj_cutoff,
  FCcutoff = lfc_cutoff,
  subtitle = sprintf(
    "Adjusted p-value cutoff = %0.2f
|Log2FoldChange| cutoff = %0.1f",
    padj_cutoff, lfc_cutoff
  )
)

iPSC_vs_MEF

# Datatable example
res <- lfc_dfs[[6]]
padj_cutoff <- 0.01
lfc_cutoff <- 0.5

res %>%
  select(SYMBOL, log2FoldChange, padj) %>%
  filter(padj <= padj_cutoff & abs(log2FoldChange) >= lfc_cutoff) %>%
  arrange(padj) %>% 
  DT::datatable() %>%
  DT::formatSignif(columns = 2:3, digits = 3)

# Volcano plot example
EnhancedVolcano::EnhancedVolcano(
  res,
  lab = res$SYMBOL,
  x = "log2FoldChange",
  y = "padj",
  pCutoff = padj_cutoff,
  FCcutoff = lfc_cutoff,
  subtitle = sprintf(
    "Adjusted p-value cutoff = %0.2f
|Log2FoldChange| cutoff = %0.1f",
    padj_cutoff, lfc_cutoff
  )
)

ESC_vs_MEF

# Datatable example
res <- lfc_dfs[[7]]
padj_cutoff <- 0.01
lfc_cutoff <- 0.5

res %>%
  select(SYMBOL, log2FoldChange, padj) %>%
  filter(padj <= padj_cutoff & abs(log2FoldChange) >= lfc_cutoff) %>%
  arrange(padj) %>% 
  DT::datatable() %>%
  DT::formatSignif(columns = 2:3, digits = 3)

# Volcano plot example
EnhancedVolcano::EnhancedVolcano(
  res,
  lab = res$SYMBOL,
  x = "log2FoldChange",
  y = "padj",
  pCutoff = padj_cutoff,
  FCcutoff = lfc_cutoff,
  subtitle = sprintf(
    "Adjusted p-value cutoff = %0.2f
|Log2FoldChange| cutoff = %0.1f",
    padj_cutoff, lfc_cutoff
  )
)